The complete mitochondrial genome characterization of Thunnus obesus (Scombriformes: Scombridae) and phylogenetic analyses of Thunnus

Comparative Mitogenomic Analysis of Heptageniid Mayflies (Insecta: Ephemeroptera): Conserved Intergenic Spacer and tRNA Gene Duplication

Large intergenic spacers and tRNA gene duplications have been reported in several insect groups, although little is known about mitogenomes of mayflies. Here, we determined complete mitogenomes of ten heptageniid species and systemically analyzed their mitogenomic features. Both a conserved intergenic spacer (IGS) and trnM duplication were detected in those mitogenomes. The IGS, which was observed in heptageniids, could be further folded into a stable stem-loop structure. The tRNA gene duplication was found in almost all analyzed mitogenomes, and a unique gene block trnI-trnM-trnQ-trnM-ND2 was also discovered. Our analysis demonstrates that the heptageniid gene arrangement pattern can be explained by the tandem duplication-random loss (TDRL) model. Phylogenetic analyses using both Bayesian inference (BI) and maximum likelihood (ML) methods based on the nucleotide and amino acid sequence data recovered the genus Epeorus as monophyletic with strong support. Our results provide a better understanding of mitogenomic evolution in Heptageniidae, as well as novel molecular markers for species identification of mayflies.

Phylogenetic analysis of the complete mitochondrial genome of Orestias ascotanensis (Cyprinodontiformes, Cyprinodontidae)

The complete mitochondrial genome of this species was first determined in this study, which is 16,617 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, a putative control region, and 1 origin of replication on the light-strand. The overall base composition includes C(27.11%), A(26.68%), T(29.15%), G(17.04%) and three degenerate bases are R, R and S. Moreover, the 13 PCGs encode 3800 amino acids in total, 12 of which use the initiation codon ATG except COI that uses GTG. Most of them have TAA as the stop codon, whereas ND5 ends with AGA, four protein-coding genes (ND1, ND2, ND3 and Cytb) ended with TAG, and two protein-coding genes (COII and ND4) ended with the incomplete stop codon represented as a single T. The phylogenetic tree based on the Neighbor Joining method was constructed to provide relationship within Cyprinodontidae, which could be a useful basis for management of this species.

Complete mitochondrial genome of Ophichthus brevicaudatus reveals novel gene order and phylogenetic relationships of Anguilliformes

Generally, a teleostean group possesses only one type or a set of similar mitochondrial gene arrangement. However, two types of gene arrangement have been identified in the mitochondrial genomes (mitogenomes) of Anguilliformes. Here, a newly sequenced mitogenome of Ophichthus brevicaudatus (Anguilliformes; Ophichthidae) was presented. The total length of the O. brevicaudatus mitogenome was 17,773 bp, and it contained 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNA (tRNA) genes, and two identical control regions (CRs). The gene order differed from that of the typical vertebrate mitogenomes. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The duplication-random loss model was adopted to explain the gene rearrangement events in this mitogenome. The most comprehensive phylogenetic trees of Anguilliformes based on complete mitogenome was constructed. The non-monophyly of Congridae was well supported, whereas the non-monophyly of Derichthyidae and Chlopsidae was not supported. These results provide insight into gene arrangement features of anguilliform mitogenomes and lay the foundation for further phylogenetic studies on Anguilliformes.

Characterization of the complete mitochondrial genome of Wuhaniligobius polylepis (Gobiiformes: Gobiidae) and phylogenetic studies of Gobiiformes

The environmental changes mainly caused by water pollution and human activities have dramatically threatened the survival of the small-scaled Wu’s goby W. polylepis. In the present study, the complete mitogenome of Wuhaniligobius polylepis was determined, which is 16,496 bp in length, containing 13 PCGs, two rRNA genes, 22 tRNA genes and a putative control region. The overall base composition is 28.6%, 29.0%, 26.7%, and 15.7% for A, T, C and G, respectively. The 13 PCGs encode 3,802 amino acids in total, twelve of which use the initiation codon ATG except COI, which uses GTG. In order to explore the systematic status of W. polylepis and further phylogenetic study of Gobiiformes, a maximum-likelihood tree was constructed based on the concatenated sequences of 12 PCGs. The result showed that Pseudogobius, Hemigobius, and Mugilogobius clustered into a clade and then formed a sister-group with W. polylepis, suggesting the invalid former name of M. polylepis or E. polylepis.

The complete mitochondrial genome sequence of Halichoeres nigrescens (Labriformes: Labridae)

The complete mitochondrial genome of marine fish Halichoeres nigrescens was sequenced by the high-throughput sequencing method. The genome is 17,252 bp in length, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one large non-coding region. The gene arrangement of Halichoeres nigrescens is identical to that of common fishes. Phylogenetic tree based on 13 protein-coding genes shows that Halichoeres nigrescens has a closer phylogenetic relationship to Macropharyngodon negrosensis than to Halichoeres hartzfeldii.

The complete mitochondrial genome sequence of Abudefduf Bengalensis (Perciformes; Pomacentridae)

The complete mitochondrial genome of marine fish Abudefduf bengalensis was sequenced by the high throughput sequencing method. The genome of this species is 16,776 bp in length, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one large non-coding region. The gene arrangement of A. bengalensis is identical to that of other common fishes. Phylogenetic tree based on 13 protein-coding genes shows that the clade of genus Abudefduf has a closer phylogenetic relationship to the lineage of genus Amphiprion and Premnas biaculeatus than to Labracinus cyclophthalmus.

Phylogenetic analysis of the complete mitochondrial genome of Anguilla japonica (Anguilliformes, Anguillidae)

The Japanese eel (Anguilla japonica), which was listed as Endangered (EN) under the International Union for the Conservation of Nature due to the declines in its abundance, overfishing, and its narrow range distribution. To better protect this species, we described the complete mitogenome of A. japonica in this study. The mitogenome is 16717bp in length and contains 13PCGs, two rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, and a putative control region (CR) and one origin of replication on the light-strand (OL). Moreover, the 13 PCGs encode 3813 amino acids in total, all the protein-coding genes use the initiation codon ATG except COI uses GTG. Most of them have TAA or TAG as the stop codon, except COI uses AGG and two PCGs (COII and ND4) use an incomplete stop codon T. A phylogenetic tree based on the Neighbour Joining method was constructed to provide relationship within Anguilla, which could be a useful basis for conservation of this species.

The complete mitochondrial genome sequence of Pelates quadrilineatus (Perciformes: Terapontidae)

The complete mitochondrial genome of marine fish Pelates quadrilineatus was sequenced by the high throughput sequencing method. This genome was 16,823 bp in length, consisted of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one large non-coding region. The gene arrangement of P. quadrilineatus is identical to those of other fishes. Phylogenetic tree based on 13 protein coding genes shows that Terapontidae has a closer phylogenetic relationship to Pentacerotidae than to Chaetodontidae.

The complete mitochondrial genome of Gymnogobius Petschiliensis (Gobiiformes; Gobiidae; Gobionellinae) and its phylogenetic implications

Of the goby fishes, many Gymnogobius species have been poor recognized mainly because of the absence of enough molecular information and clear phylogenetic framework. In this study, the complete mitochondrial genome of Gymnogobius petschiliensis was determined and described. The mitogenome is 16,422 bp in length and consists of 22 tRNAs, 13 protein-coding genes, two rRNAs, one control region and a light strand replication origin (O_L). The arrangement of this mitogenome is identical to that of the typical teleost. The overall base composition is 27.5%, 29.5%, 26.1%, and 16.9%, for A, T, C, and G, respectively, with a slight bias on A + T content (57.0%). The 13 protein-coding genes use the initiation codon ATG except COI, which uses GTG. Most of them use TAA or TAG as the stop codon, while COII, COIII, and Cyt b use an incomplete T or TA and ND4 uses an unusual AGA. The maximum-likelihood phylogeny tree of 19 Gobionellinae species demonstrated that G. petschiliensis had a very closely relationship with the same genus G. urotaenia. This study is expected to contributing to the phylogenetic evolution of G. petschiliensis and further phylogenetic relationship of Gobionellinae and Gobiiformes.